One of the standard defences of the selfish gene view is
based on the discovery that, in humans and many other
organisms, only a few per cent of the genome codes for
proteins and can therefore be classified as ‘genes’ in the
usual sense. The rest was described as ‘junk’ DNA, the
ultimate example of ‘selfishness’ since it was seen as DNA
‘hitching a ride’ with no function, a bit like a virus that
has become permanently resident in the body. The strong
implication is that this discovery favours the selfish gene
view.

I think that is a confusing way of viewing genomes. There
are several ways in which the confusion can be unravelled.

The words ‘selfish’, ‘junk’, etc. are, of course, metaphors.
More importantly they are empirically empty metaphors when
applied to sequences of DNA. No conceivable experiment could
validate or invalidate them. The reasons are fully explained
in
Noble (2011).See also the answer to ‘what
is wrong with The
Selfish Gene?’
in this document.

That the metaphors are empty, however, does not mean that
they have no impact. On the contrary, they have had, and
still have, very persuasive impact on the way in which many
people think about biology.
The Selfish Gene
sells in millions of copies. Its impact extends way beyond
biology, into economics, politics and business studies.

A more persuasive counter-argument is therefore needed, and
what might persuade most people is experimental evidence
favouring a different view. Fortunately, recent experimental
work has provided us with precisely that. The more we
examine non-protein-coding DNA the more evidence we find
that an overwhelming 80% is transcribed to form RNAs, and
that around 20% are already known to have function
(http://www.genome.gov/10005107).

Mobile genetic elements have also been characterised as “
selfish” and “parasitic”. Yet they account for nearly 20% of
“all conserved (i.e. positively selected) differences
between eutherian mammals and marsupials (Lindblad
et al , 2011).”
For further debate on these issues the reader is referred to
the series of articles (July 2013) in
Physics of Life Reviews.